All metazoans examined to date contain families of repetitive DNA sequences, and suggestions for their function include coordination of the expression of tissue-specific genes, promotion of chromosomal rearrangements such as duplications, inversions, and deletions, a role in speciation, or even no function except self-propagation as "selfish" DNA. We have developed an experimental approach to rapidly characterize and identify rat repeated DNA sequences of potential interest, and in our earlier studies we identified a number of highly repeated, transcribed DNA sequences that appear to be organized as permuted clusters. In examining the genomic regions that contain these sequences we found that one class of them is located in long, 3-7 kb structures that are themselves repeated about 50,000 times in the rat genome. These structures are the counterparts in rats of long interspersed repeated elements (referred to as LINES) that have been identified in mice and primates. We have determined their overall structure and found that, although they are quite polymorphic, they share common architectural features as revealed by the spacing of certain restriction enzymes sites. In addition we have shown that rat LINES appear to be mobile in the rat genome since they produce heterozygosity among individual rats of different laboratory strains as well as of wild rats. Three such loci are the murine leukemia virus integration site 2, the immunoglobulin heavy chain locus, and the rat insulin I locus. The latter case is particularly intriguing because amplification of the rat insulin I locus and flanking DNA accompanies the presence of the rat LINE. We also found that rat repeated sequences can be classified as either "G:C-rich" or "A:T-rich". The latter are the ones that comprise rat LINES, and genomic regions that contain LINES contain few, if any, of the G:C-rich sequences. On the other hand, the regions of the genome that contain multiple copies of the G:C-rich sequences appear to lack LINES. In an attempt to confirm the impression that G:C-rich and A:T-rich repeated sequences are segregated in the genome, we are using in situ hybridization to map the G:C-rich and A:T-rich repeated sequences at the chromosomal level.